Biomarkers for Cervical Cancer

ABSTRACT

The invention relates to methods, reagents and kits for detecting the susceptibility to cervical cancer. In particular, it relates to novel methylation markers to improve screening for cervical intraepithelial neoplasia grade 2/3 (CIN2/3) and the use thereof for identifying a cervical cell as neoplastic or predisposed to neoplasia in an isolated sample.

RELATED APPLICATIONS

The instant application is a divisional of U.S. patent application Ser.No. 15/511,767, filed Mar. 16, 2017, which is a National StageApplication under 35 U.S.C. 371 of expired PCT applicationPCT/NL2015/050650 designating the United States and filed Sep. 21, 2015;which claims the benefit of EP application number 14185831.6 and filedSep. 22, 2014, each of which are hereby incorporated by reference intheir entireties.

The invention relates to methods, reagents and kits for detecting thesusceptibility to cervical cancer. In particular, it relates to novelmethylation markers to improve screening for cervical intraepithelialneoplasia grade 2/3 and the use thereof for identifying a cervical cellas neoplastic or predisposed to neoplasia in an isolated sample.

Cervical cancer is characterized by a well-defined pre-malignant phase,cervical intraepithelial neoplasia (CIN). Identification of these CINlesions by population-based screening programs and their subsequenttreatment has led to a significant reduction of the incidence andmortality of cervical cancer^(1,2). Cytology-based testing of cervicalsmears is the most widely used cervical cancer screening method, but isnot ideal, as the sensitivity for detection of CIN2 and higher (CIN2+)is only ˜55%³⁻⁵. Cervical carcinogenesis is highly associated withhigh-risk human papillomavirus (hrHPV)⁶. Large randomized-controlledtrials have shown that the sensitivity of hrHPV testing is significantlyhigher than cytology testing^(4,7-10). However, the specificity of hrHPVtesting, especially in a young screening population is relativelylow^(3,11-13), which may lead to unnecessary referrals to thegynecologist, anxiety in the false-positive women, and higher costs forthe health-care system. Finally, in the near future the prevalence ofCIN and cervical cancer will probably decrease in countries that haveintroduced primary prevention with hrHPV vaccination. With this decreasein prevalence, the positive predictive value of the current screeningtests will by definition decrease¹⁴. Therefore, other objectivebiomarkers with both high sensitivity as well as high specificity areneeded as new screening tools for cervical cancer.

Different DNA methylation patterns in normal versus (pre)malignantlesions represent excellent targets for diagnostic approaches based onmethylation specific PCR (MSP). Promoter hypermethylation of tumorsuppressor genes is an early event in cervical carcinogenesis andconsequently hypermethylation analysis can be especially relevant forthe early detection of cervical neoplasia¹⁵⁻¹⁷. Assessment ofmethylation markers in cervical scrapings for the detection of CIN andcervical cancer is feasible¹⁷⁻²³. See also WO2006/007980. However,finding methylation markers with both high sensitivity as well as highspecificity remains a challenge.

Through the years gradually more sophisticated approaches have beendeveloped to identify new methylation markers on a genome-wide scale²⁴.Amidst comparable studies from other groups we have previously reportedour experience with pharmacological unmasking of the promoter regioncombined with re-expression as analyzed by microarrays, high-throughputquantitative methylation specific PCR (QMSP) on an OpenArray platformand methyl-DNA immunoprecipitation followed by microarray analysis(MeDIP), resulting in the discovery and validation of the genesC13ORF18, JAM3, EPB41L3 and TERT^(21,22,25). See also WO2009/115615. Thediagnostic performance of these genes showed sensitivities for detectingCIN2+ in a hrHPV positive population between 43%-71% and specificitiesbetween 89%-100%²¹. However, strategies for discovering new methylationmarkers so far were based on the difference between cancer and normaltissue resulting in markers with high sensitivity for carcinoma, butwith too low sensitivity for detecting CIN2/3 lesions. In our MeDIPstudy DNA methylomes of normal and CIN3 lesions were analyzed²⁵.However, a disadvantage of this technique is that it primarilyrecognizes bulk quantities of highly methylated repetitive DNA,resulting in less specificity.

Accordingly, the present inventors set out to identify and validate newmethylation markers that can differentiate between normal cervices andCIN2/3 lesions. To that end, a novel and more specific innovativegenome-wide methylation analysis of DNA from CIN2/3 lesions versusnormal cervical tissue was developed. Methylated-CpG island recoveryassay (MIRA) using antibody-coupled methyl-binding domain (MBD) of humanMeCP2 to specifically purify methylated DNA was applied. The higheraffinity of the MBD complex for double-stranded CpG-methylated DNAresults in a higher enrichment for methyl DNA sequences as compared toMeDIP analysis. Next-generation-sequencing then revealed the identifiednovel methylated regions (MethylCap-seq). Diagnostic evaluation incervical scrapings showed that for 8 newly identified genes the relativelevel of methylation increases with the severity of the underlyinghistological lesion. The novel methylation markers can be advantageouslyapplied as a triage test in hrHPV positive women from population-basedscreening. A combination of markers was found to provide an improveddiagnostic value.

In one embodiment, the invention provides a method of identifying acervical cell as neoplastic or predisposed to neoplasia in an isolatedsample, comprising determining the methylation status of at least twomarker genes selected from the group consisting of KCNIP4, GATA4, GFRA1,ST6GALNAC5, CDH6, ZSCAN1, ANKRD18CP (also known in the art asAL590705.4) and LHX8.

More specifically, it was found that hypermethylation of these genes isindicative for cervical cancer. Accordingly, a method according to theinvention preferably comprises determining whether said marker genes arehypermethylated, herein also referred as “methylation positive”.

Some of the above markers have been individually implicated in disease.For example, WO2009/115615 discloses a set of 111 individual markers,among which GATA4, whose methylation status is linked to cervicalcancer. Analysis of the methylation status of either KCNIP4, GFRA1,ST6GALNAC5, CDH6 or ZSCAN1 is reported in the art for various types ofcancer. However, their prognostic value for cervical cancer was neverdisclosed. The prior art is completely silent about a link between themethylation status of ANKRD18CP or LHX8 and disease. Thus, theprognostic value of a marker gene combination of the present inventionfor identifying cervical neoplasia (CIN2/3) is not disclosed orsuggested in the art.

In one embodiment, a method of the invention comprises determining themethylation status of at least KCNIP4, and/or at least GATA4, and/or atleast GFRA1, and/or at least ST6GALNAC5, and/or at least CDH6, and/or atleast ZSCAN1, and/or at least ANKRD18CP, and/or at least LHX8. Preferredcombinations of two methylation markers include ANKRD18CP and CDH6;GFRA1 and CDH6; and GFRA1 and ANKRD18CP.

The accession numbers corresponding to the listed genes can be found atthe National Center for Biotechnology Information website. Of course, asappropriate, the skilled person would appreciate that functionallyrelevant variants of each of the gene sequences may also be detectedaccording to the methods of the invention. For example, the methylationstatus of a number of splice variants may be determined according to themethods of the invention. Variant sequences preferably have at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, or at least 99%nucleotide sequence identity with the nucleotide sequences in thedatabase entries. Computer programs for determining percentagenucleotide sequence identity are available in the art, including theBasic Local Alignment Search Tool (BLAST) available from the NationalCenter for Biotechnology Information.

In one embodiment, the method comprises determining the methylationstatus of at least three, preferably at least four, more preferably atleast five marker genes selected from the group consisting of KCNIP4,GATA4, GFRA1, ST6GALNAC5, CDH6, ZSCAN1, ANKRD18CP and LHX8. For example,each of the following marker gene combinations can be used:

-   -   GFRA1, ANKRD18CP and CDH6;    -   GFRA1, ANKRD18CP and LHX8.    -   GFRA1, CDH6, and LHX8.    -   GFRA1, CDH6, ANKRD18CP and LHX8.    -   GFRA1, CDH6, ZSCAN1, and ANKRD18CP.    -   GFRA1, CDH6, ZSCAN1, ANKRD18CP and LHX8.

In one preferred aspect, the methylation status of at least KCNIP4,ST6GALNAC5 and/or ZSCAN1 is determined. In another preferred aspect, themethylation status of at least one of CDH6, GATA4 and LHX8 is detected.In yet another preferred aspect, the methylation status of at least oneof GFRA1 and ANKRD18CP, or at least one of ANKRD18CP and LHX8 isdetected.

In a specific embodiment, the methylation status of KCNIP4, GATA4,GFRA1, ST6GALNAC5, CDH6, ZSCAN1, ANKRD18CP and LHX8 is determined.

It is possible for the methods of the invention to be used in order todetect more than one gene of interest in the same reaction. Through theuse of several specific sets of primers, amplification of severalnucleic acid targets can be performed in the same reaction mixture. Thismay be termed “multiplexing”. Multiplexing can also be utilized in thecontext of detecting both the gene of interest and a reference gene inthe same reaction.

As will be understood, the marker panel of the invention can be combinedor supplemented with any marker gene or marker gene combination known inthe art to be for useful for identifying, diagnosing, prognosing, and/orscreening for cervical cancer. See for example WO2004/087957WO2006/007980, WO2009/115615 or WO2011/036173.

Combining the newly identified genes with our previously reported panel(C13ORF18, JAM3, EPB41L3 and TERT; see WO2011/036173) surprisinglyrevealed that for the combinations JAM3/ANKRD18CP,C13ORF18/JAM3/ANKRD18CP and JAM3/GFRA1/ANKRD18CP sensitivities for CIN2+are between 72-74%, which is comparable to the sensitivity for CIN2+ ofhrHPV testing (79%). Specificities of our gene panel was between 76-79%,which is significantly higher (p≤0.05) than the specificity for hrHPVtesting (42%) in a triage setting after a positive Pap smear test resultin population-based screening.

Accordingly, in one embodiment, the panel of marker genes furthercomprises at least one of JAM3, EPB41L3 and C13ORF18. For example, itcomprises determining the methylation status of the genes of at leastone of the following panels of marker genes:

-   -   ANKRD18CP, CDH6 and EPB41L3    -   GFRA1, EPB41L3 and CDH6;    -   GFRA1, ANKRD18CP and CDH6;    -   GFRA1, EPB41L3 and ANKRD18CP;    -   JAM3, GFRA1 and ANKRD18CP.

Also provided herein is a method of identifying a cervical cell asneoplastic or predisposed to neoplasia in an isolated sample, comprisingdetermining the methylation status of a panel of at least a first andsecond marker genes, wherein the at least first marker gene is selectedfrom the group consisting of KCNIP4, GFRA1, ST6GALNAC5, CDH6, ZSCAN1,ANKRD18CP and LHX8, and wherein the at least second marker gene isselected from JAM3, EPB41L3 and C13ORF18. Preferably, the marker genepanel comprises at least one of the following combinations of markergenes:

JAM3/CDH6; ANKRD18CP/CDH6/EPB41L3; GFRA1/EPB41L3/CDH6; CDH6/EPB41L3;JAM3/EPB41L3/ANKRD18CP; C13ORF18/JAM3/ANKRD18CP;GFRA1/EPB41L3/ANKRD18CP; ANKRD18CP/EPB41L3; C13ORF18/CDH6;JAM3/GFRA1/ANKRD18CP; C13ORF18/JAM3/EPB41L3; JAM3/ANKRD18CP;JAM3/EPB41L3/GFRA1; GFRA1/EPB41L3; C13ORF18/JAM3/GFRA1; JAM3/GFRA1 andC13ORF18/ANKRD18CP.

As shown herein below, a method according to the invention allowsdetection of CIN2 or higher (CIN2+) cervical cancer with increasedsensitivity and/or increased specificity over existing methods. In oneembodiment, it allows detection of CIN2+ cervical cancer with asensitivity and/or a specificity of at least 65%, preferably at least70%. For example, both sensitivity and specificity are at least 66%,67%, 68%, 69%, 70%, 71%, 72%, 73%, 74% or 75%.

The sample to be analyzed can be a cervical scraping, preferably aself-collected vaginal swab, or wherein the sample is a liquid basedcytology sample.

The advantage of methylation analysis is that is an objective test andthat it can be performed on the same material used for hrHPV testing,which makes it also interesting for self-sampled material. Differentmethylation markers already have been tested as a triage test in hrHPVpositive women. However, for most markers a cut-off value was set inorder to obtain high specificity. The advantage of the newly foundmarkers is that no cut-off value is needed. If the PCR product isnegative (i.e. no amplification of specific product), the samples arecalled negative and any ratio above zero is called positive. This uniquefeature of the selected genes allows an objective and easy to interprettest.

Methods to determine the methylation status of the marker genes areknown in the art. In one embodiment, at least one pair ofoligonucleotide primers is designed not to contain cytosines andamplifies modified and unmodified sequences. An additional amplificationmay be subsequently performed with primers hybridizing to the modifiedsequence, thereby indicating methylation; or alternatively a detectionstep with a specific probe may be performed, thereby indicatingmethylation. Alternatively, the amplification may be combined withrestriction cutting by using methylation sensitive enzymes; only themethylated region is amplified in this case.

Alternatively, methylation-sensitive restriction endonucleases can beused to detect methylated CpG dinucleotide motifs. Such endonucleasesmay either preferentially cleave methylated recognition sites relativeto non-methylated recognition sites or preferentially cleavenon-methylated relative to methylated recognition sites. Alternatively,chemical reagents can be used that selectively modify either themethylated or non-methylated form of CpG dinucleotide motifs, therebytransforming the CpG-dinucleotide motifs. Modified products can bedetected directly, or after a further reaction which creates productsthat are easily distinguishable. Means which detect altered size andcharge can be used to detect modified products, including but notlimited to electrophoresis, chromatography, and mass spectrometry.Examples of such chemical reagents for selective modification includehydrazine and bisulfite ions. Hydrazine-modified DNA can be treated withpiperidine to cleave it. Bisulfite ion-treated DNA can be treated withalkali. In one embodiment of the present invention, methylation isdetected by contacting at least a portion of the applicable gene orpromoter region thereof with a chemical reagent that selectivelymodifies a non-methylated cytosine residue relative to a methylatedcytosine residue, or selectively modifies a methylated cytosine residuerelative to a non-methylated cytosine residue; and detecting a productgenerated due to said contacting. In a further embodiment, the chemicalreagent comprises bisulfite ions. In a further embodiment, the methodfurther comprises treating with alkali the bisulfite ion-contactedportion of the gene.

Other means for detection that are reliant on specific sequences can beused, including but not limited to electrophoresis, hybridization,amplification, quantitative methylation-specific PCR (QMSP), sequencing,ligase chain reaction, chromatography, mass spectrometry. Combinationsof such techniques may also be used.

In a preferred embodiment, a method of the invention involvesdetermining the methylation status of the genes using methylationspecific PCR (MSP), preferably real-time quantitative methylationspecific PCR (QMSP). To adjust for DNA input, hypermethylation ratiosare advantageously calculated against DNA levels of a reference gene,for instance beta-actin or beta-catenin.

In a specific aspect, the methylation status is determined using a setof primers comprising or consisting of a sequence selected from entries1-16 of Table 1A and/or a probe comprising or consisting of a sequenceselected from entries 17-24 of Table 1B.

In a related embodiment, the invention provides for a method forcervical cancer detection or screening comprising the steps of: a)performing cytology evaluation on a test sample comprising cervicalcells or nucleic acids from cervical cells; b) if a) is positive,assaying the methylation status of at least two genes selected from thegroup consisting of KCNIP4, GATA4, GFRA1, ST6GALNAC5, CDH6, ZSCAN1,ANKRD18CP and LHX8; c) if the at least two genes of b) are methylated,refer the woman for colposcopy; d) if the at least two genes of b) areunmethylated, refer the woman to cytology testing on a more regularbasis.

In a related embodiment, the invention provides for a method forcervical cancer detection or screening comprising the steps of: a)assaying the methylation status of at least two genes selected from thegroup consisting of KCNIP4, GATA4, GFRA1, ST6GALNAC5, CDH6, ZSCAN1,ANKRD18CP and LHX8; b) if the at least two genes of a) are methylated,perform cytology testing; c) if b) is tested positive, refer the womanfor colposcopy; d) if b) is negative, refer the woman to follow-up after6 month for HPV-testing.

The invention also relates to a kit for use in identifying a cervicalcell as neoplastic or predisposed to neoplasia, preferably cervicalneoplasia (CIN2/3), in an isolated sample. A kit of the invention ischaracterized by the presence of gene specific primers for at least twogenes selected from the group consisting of KCNIP4, GATA4, GFRA1,ST6GALNAC5, CDH6, ZSCAN1, ANKRD18CP and LHX8; gene specific probes forsaid at least two genes; and preferably a tool for removing cervicalcells from a subject, such as an Ayre's spatula and/or an endocervicalbrush.

In another embodiment, the kit comprises gene specific primers for of atleast two marker genes, wherein the at least first marker gene isselected from the group consisting of KCNIP4, GFRA1, ST6GALNAC5, CDH6,ZSCAN1, ANKRD18CP and LHX8, and wherein the at least second marker geneis selected from JAM3, EPB41L3 and C13ORF18; gene specific probes forsaid at least two genes; and optionally an Ayre's spatula and/or anendocervical brush for removing cervical cells from a subject.

Preferably, the kit comprises gene specific primers for at least one ofthe following combinations of marker genes:

JAM3/CDH6; ANKRD18CP/CDH6/EPB41L3; GFRA1/EPB41L3/CDH6; CDH6/EPB41L3;JAM3/EPB41L3/ANKRD18CP; C13ORF18/JAM3/ANKRD18CP;GFRA1/EPB41L3/ANKRD18CP; ANKRD18CP/EPB41L3; C13ORF18/CDH6;JAM3/GFRA1/ANKRD18CP; GFRA1/CDH6; JAM3/ANKRD18CP; JAM3/EPB41L3/GFRA1;GFRA1/EPB41L3; C13ORF18/JAM3/GFRA1; JAM3/GFRA1; and C13ORF18/ANKRD18CP.

Preferred primers and probes for use in a kit of the invention areselected from the primers and probes comprising or consistingessentially of the nucleotide sequences set forth in Table 1A or 1B. Inone embodiment, the kit comprises one or more gene specific primer(s)comprising or consisting of a sequence selected from entries 1-16 ofTable 1A. Alternatively or additionally, the kit comprises at least onegene specific probe comprising or consisting of a sequence selected fromentries 17-24 of Table 1B.

Related to this, the invention also provides for an isolatedpolynucleotide which consists of a nucleotide sequence listed in Table1A or Table 1B.

The kit may additionally comprising gene specific reagents for furthergene(s) whose methylation status is linked to the incidence of cervicalcancer, preferably wherein said further gene(s) comprises JAM3, EPB41L3and/or C13ORF18.

LEGENDS TO THE FIGURES

FIG. 1: Flow scheme of the strategy used for the identification of newCIN2+ methylation markers.

FIG. 2: Methylation ratio of 9 genes tested with QMSP in scrapings fromnormal (NI) and cancer (Ca) patients. Relative levels of methylation issignificantly higher in the cancer scrapings (all genes, except PAX2,p<0.001).

FIG. 3: ROC curve analyses of methylation ratio's per gene.

FIG. 4: Methylation ratio of each of 8 novel marker genes tested withQMSP in scrapings from patients with CIN0, CIN1, CIN2, CIN3 and (mi)Ca.Relative levels of methylation significantly increase with more severehistological abnormality (all p<0.001).

EXPERIMENTAL SECTION

Patients and Methods

General Strategy

To characterize the DNA methylome of CIN2/3 lesions and to identify newCIN2 or higher (CIN2+) methylation markers, we applied the followingstrategy (see FIG. 1): First, methylated DNA was enriched using MBD ofhuman MECP2 with subsequent paired-end sequencing (MethylCap-seq) on DNAisolated from fresh-frozen macro-dissected epithelial tissue of 18CIN2/3 lesions (6 CIN2 and 12 CIN3), 20 normal cervices and two pools ofleukocyte DNA of healthy volunteers. In order to identify differentialmethylated regions (DMRs), we retrieved the reads of promoter and exonregions. We selected methylation markers that showed significantdifferences between the normal and CIN2/3 cervices, while also theleukocyte count had to be low, to prevent false-positive results.Markers were ranked on high specificity (no methylation in the normalcervices) and high sensitviy (methylation in CIN2/3 lesions). For thehighest ranking top15 genes, methylation specific PCR (MSP) primers weredesigned and methylation patterns were verified on the same DNA, whichoriginally was used for MethylCap-seq. This first validation stepenabled verification of MethylCap-seq data by correlating MSP bandintensity with the number of reads from the MethylCap-seq. In the secondvalidation step high prevalence of methylation in the CIN2/3 lesions andno methylation in the normal cervices was analyzed by MSP analysis onDNA isolated from a completely independent cohort of patients (cervicalcancer (n=13), CIN2/3 lesions (n=19) and normal cervices (n=17)). DNAwas isolated from macro-dissected formalin fixed paraffin embedded(FFPE) epithelial tissue.

Finally, diagnostic evaluation of the newly discovered methylationmarkers was performed by QMSP on cervical scrapings. First, we testedthe methylation ratios of new biomarkers on a large series of randomlyselected scrapings from cervical cancer patients (n=100) and a similarage group of healthy controls (n=89). Secondly, the potential of the newmethylation markers as a diagnostic tool was evaluated in a large seriesof scrapings (n=215) of randomly selected patients, referred with anabnormal Pap smear at population-based screening. Histology was used asthe reference standard.

Patient Samples

All patients referred to the outpatient clinic of the University MedicalCenter Groningen (UMCG) with cervical cancer or an abnormal Pap smear atpopulation-based screening are routinely asked to participate in ourongoing ‘Methylation study’ which has been approved by the InstitutionalReview Board (IRB) of the UMCG. Cervical tissue, scrapings andclinicopathologic data are prospectively collected and stored in ourtissue bank. Within our Methylation study tissue samples, scrapings andclinicopathologic data from normal cervices are also collected frompatients planned to undergo a hysterectomy for non-malignant reasons.All cervical tissue that was used for the normal control group wasjudged as histopathological normal. Patients referred with cervicalcancer are staged according to the FIGO criteria with pelvic examinationand biopsies under general anaesthesia. Cervical scrapings from bothgroups (cervical cancer staging and benign gynecologic surgery) werecollected before surgery under general anaesthesia. All patientsreferred with an abnormal Pap smear at population-based screeningunderwent an additional Pap smear prior to colposcopy specifically forthis study. At colposcopy, biopsies and/or Large Loop Excision of theTransformation Zone (LLETZ) were performed. The tissue samples werescored by an experienced gynaecologic pathologist and the histologicalclassification was used as the reference standard. If no interferencewith routine diagnostic evaluation was anticipated, specimens from theCIN lesions were retrieved and stored at −80° C. Clinicopathologicaldata were retrieved from patient files and stored in our large anonymouspassword-protected institutional Gynecologic Oncology database. Allpatients gave written informed consent.

For the frozen tissue samples used in de MethylCap-seq analysis, themedian age of the CIN2/3 patients was 35 years (IQR 30-39) and for thepatients with normal cervices 43 years (IQR 41-44). For the independentcohort of patients with FFPE samples, the median age of the CIN2/3patients was 37 years (IQR 34-41), for the patients with normal cervices43 years (IQR 40-44) and for the cervical cancer patients 49 years(range 42-54). For the cervical scrapings the median age of cervicalcancer patients was 50 years (IQR 39-64) and for the patients withnormal cervices 47 years (IQR 43-53). The stage of cervical cancerpatients was: 1 (1%) FIGO stage IA1, 31 (31%) FIGO stage IB1, 18 (18%)FIGO stage IB2, 21 (21%) FIGO stage IIA, 17 (17%) FIGO stage IIB, 1 (1%)FIGO stage IIIA, 8 (8%) FIGO stage IIIB and 3 (3%) FIGO stage IV.Histological classification of the cervical cancer patients was: 70(70%) squamous cell carcinoma (SCC), 21 (21%) adenocarcinoma (AD), 3(3%) adenosquamous (ASC) and 6 (6%) undifferentiated carcinoma. Themedian age of the patients referred with an abnormal Pap smear was 37years (IQR 32-43). The histological classifications of these patientswere: 27 without CIN, 38 CIN1, 45 CIN2, 61 CIN3 and 44 miCa (29 SCC, 12AD, 3 ASC). The Pap smears were classified according to the Papanicolaousystem. Table 4 shows per histological subgroup, the Pap classification(and translation to Bethesda).

From all frozen tissue samples used for MethylCap-seq and the FFPEsamples, 10 m tissue sections were cut and macrodissection was performedto enrich for epithelial cells. Before and after cutting a hematoxylinand eosin slide was made to check presence of epithelial cells. Cervicalscrapings were collected in 5 ml ice-cold phosphate buffered saline(PBS: 6.4 mM NA₂HPO₄; 1.5 mM KH₂PO₄; 0.14 M NaCl; 2.7 mM KCl) and kepton ice until further processing. Of these 5 ml cell suspension, 1 ml wasused for cytomorphological assessment. The remaining 4 ml wascentrifuged and the cell pellet was suspended in 1 ml TRAP wash bufferand divided in 4 fractions. Two fractions were stored as dry pellet at−80° C. for DNA isolation as described previously²¹.

DNA Isolation

Tissue slides from FFPE tissue were deparaffinized using 100% xylenefollowed by 100% ethanol¹⁷. Genomic DNA from fresh-frozenmacro-dissected samples and cervical scrapings was isolated by standardovernight 1% SDS and Proteinase K treatment, salt-chloroform extractionand isopropanol precipitation as described previously²¹. DNA pelletswere washed with 70% ethanol and dissolved in 150 μl TE⁻⁴ (10 mMTris/HCL; 0.1 mM EDTA, pH 8.0). Genomic DNA was amplified in a multiplexPCR according to the BIOMED-2 protocol, to check the DNA's structuralintegrity²⁷. For the MethylCap-seq samples, DNA quantity was measuredusing Quant-iT™ PicoGreen® dsDNA Assay Kit according to manufacturer'sprotocol (Invitrogen, Carlsbad, Calif., USA). For cervical scrapings DNAconcentrations and 260/280 ratios were measured using the NanodropND-1000 Spectrophotometer (Thermo Scientific, Waltham, Mass., USA). A260/280 ratio of >1.8 was required for all samples.

Methylated-CpG Island DNA Capturing Followed by Next-GenerationSequencing (MethylCap-Seq)

Methylated DNA fragments were captured with methyl-binding domains usingthe MethylCap kit according to manufacturers instructions (Diagenode,Liège, Belgium). The kit consists of the methyl binding domain (MBD) ofhuman MeCP2, as a C-terminal fusion with Glutathione-S-transferase (GST)containing an N-terminal His6-tag. Before capturing, DNA samples (500ng) were sheared to a size range of 300-1000 bps using a Bioruptor™UCD-200 (Diagenode, Liège, Belgium) and fragments of ˜300 bp wereisolated. Leukocyte DNA of 4 healthy controls were included in 2 sets of2 samples. Captured DNA was paired-end-sequenced on the Illumina GenomeAnalyzer II platform according to protocol (Illumina, San Diego, Calif.,USA). Results were mapped on the nucleotide sequence using Bowtiesoftware²⁸, visualized using BioBix' H2G2 browser and processed usingthe human reference genome (NCBI build 37). The paired-end fragmentswere unique and located within 400 bp of each other²⁹.

MethylCap-Sequencing Analysis

For statistical analysis, reads of promoter (−2000 bp—to +500 bp oftranscription start site) and exon regions were retrieved. In order toidentify differences between normal cervices and CIN2/3 lesions, wedichotomised the read data into methylation positive or negative.Samples were considered negative if a sample showed either 0 or 1 read.Samples were considered methylation positive if a sample showed ≥3reads. Subsequently, regions were ranked based on highest specificityand highest sensitivity for CIN2/3. The candidate markers should fulfilthe following criteria: 1) Low/negative reads in the leukocytes toprevent false positive results. The region was excluded if bothleukocyte samples showed >1 read or if 1 leukocyte sample showed >2reads. 2) Unmethylated (0 or 1 read) in at least 75% (15/20) of thenormal cervix group. 3) Methylated (≥3 reads) in at least 28% (5/18) ofthe CIN2/3 lesion group.

Verification and Validation of MethylCap-Sequencing Data by MethylationSpecific PCR (MSP)

MSP primers were designed for the highest ranking top 15 genes (16DMRs). Sodium bisulfite treatment of isolated genomic DNA (1 μg/sample)was performed according to the recommendations of the EZ DNA methylationkit (Zymo, BaseClear, Leiden, the Netherlands). MSP design and analysiswas performed using sequences derived from the H2G2 browser. Eachreaction was performed in 30 μl total reaction volume, containing: 600nM of each MSP primer, 1.5 μl of bisulphite treated DNA (approximately15 ng), standard PCR components (Applied Biosystems) and 0.5 U AmpliTaqGold DNA polymerase (Applied Biosystems). Condition of the MSP was: 10min hot-start at 95° C.; 95° C. for 60 sec, 60° C. for 60 sec, 72° C. 60sec for a total of 40 cycles, with a final elongation step of 7 min at72° C. Leukocyte DNA from healthy women was used as negative control andin vitro methylated (by SssI enzyme) leukocyte DNA was used as positivecontrol for each MSP.

Quantitative Methylation Specific PCR (QMSP)

QMSP was performed as described previously by our group with an internal(FAM-ZEN/IBFQ)-labelled hybridisation probe for quantitative analyses²¹.Primer and probe sequences are summarized in Table 1. β-actin was usedas a methylation independent internal reference gene.

TABLE 1A Primer and probe sequences used in Quantitative MethylationSpecific PCR (QMSP) Gene Forward primer 5′→3′ Reverse primer 5′→3′ZSCAN1 TTGTTGGTATTCGTTTGTTC (SEQ ID ACGCGACCGAACGATATT (SEQ NO: 1)ID NO: 2) ST6GALNAC5 GTAGTTGCGGATGGAGGTTC (SEQ ID CTAACTACGCTCACCCTCCGNO: 3) (SEQ ID NO: 4) ANKRD18CP CGATGTGGTATTTTCGATTC (SEQ IDACGTCTAAAAAATCGCCAC (SEQ NO: 5) ID NO: 6) CDH6GGGCGGCGTTGTTGTC (SEQ ID NO: 7) CCAACCCCACGACGAATC (SEQ ID NO:8) GFRA1TAGGGGGAATCGATGTTTC (SEQ ID GAATCCTAAACACCGAACGA NO: 9) (SEQ ID NO: 10)GATA4 GGTCGGGTTAATTCGGTC (SEQ ID CCTCGACAAAACTCAAAACG NO: 11)(SEQ ID NO: 12) KCNIP4 GGGACGTAGGGTGTAGAAGC (SEQ IDAAACTCTCGCTCCCAACG (SEQ NO: 13) ID NO: 14) LHX8TATTTTTTTCGTAGCGGATC (SEQ ID ACGAAAAACCAAATTCTACG NO: 15)(SEQ ID NO: 16)

TABLE 1B Probe sequences used in Quantitative Methylation Specific PCR(QMSP) Gene 6FAM/ZEN/IBFQ probe 5′→3′ ZSCAN1AGGTCGAAGTTTTTTTACGTATTTTTATTGTTCGTTTA (SEQ ID NO: 17) ST6GALNAC5TTGAAGTTTCGGGTTTGGTCGTCGAGTC (SEQ ID NO: 18) ANKRD18CPAGGAGCGTTTGGTTTAGGCGTTTTTCG (SEQ ID NO: 19) CDH6CGTTTTTCGGGGAGTTTGGGTATCGTTTTTTCG (SEQ ID NO: 20) GFRA1TTTATTCGTCGCGCGTTTTCGG (SEQ ID NO: 21) GATA4ATTTCGGTGAGTAGGAGCGCGAG (SEQ ID NO: 22) KCNIP4TCGGTTAGGGGCGTTTGTTTACGGGTTTGTACGG (SEQ ID NO: 23) LHX8ATTGGCGTTTTGCGAATCGG (SEQ ID NO: 24)

QMSP reactions were performed in 10 μl final volume, containing: 300 nMof forward and reverse primers, 250 nM of hybridisation probe, 5 μl of2* QuantiTech Probe PCR Master Mix (Qiagen Hilden, Germany) and 2.5 μlbisulfite modified DNA (approximately 25 ng). Each sample was analyzedin triplicate by ABI PRISM® 7900HT Sequence Detection System (AppliedBiosystems). Negative and positive controls were the same as used forMSP. Standard curve analysis was performed on each plate and by eachprimers-probe set on serial dilutions of in vitro methylated leukocyteDNA. A DNA sample was considered methylated if at least 2 out of the 3wells were methylation positive with a Ct-value below 50 and DNA inputof at least 225 pg β-actin. The relative level of methylation of theregion of interest was determined by the following calculation: theaverage quantity of the methylated region of interest divided by theaverage quantity of the reference β-Actin gene and multiplied by10000³⁰. In our analysis we also included 4 genes previously describedby our group (C13ORF18, JAM3, EPB41L3 and TERT) to compare sensitivityand specificity of these known genes with the newly identifiedmethylation markers. QMSP for these markers was performed as previouslydescribed²¹.

HPV Testing

HrHPV testing was performed using general primer-mediated PCR (GP5+/6+)as reported previously so. For HPV-typing as well as detection of theclinical relevant HPV infections, GP5+/6+ positive cases were tested byCOBAS® 4800 HPV test. The COBAS HPV test individually detects HPV 16 and18, while at the same time identifying 12 additional hrHPV types 31. TheCOBAS HPV test is routinely used in our iso-15189-certified laboratoryof molecular pathology on scrapings from the national population-basedscreening program. For the COBAS® HPV testing in this study, the PCRonly workflow was used, since no liquid-based scrapings in Preservcyt®were available but only already isolated DNA. This workflow was firstvalidated with DNA isolated from clinical samples that were testedpreviously in the diagnostic routine and this showed comparable resultsto the liquid-based samples.

Statistical Analysis

Statistical analysis was performed using SPSS software package (SPSS 20,Chicago, Ill., USA). Spearman's rank correlation coefficient was used tocompare the MethylCap-seq reads with the MSP band intensity. Categoricalmethylation data were analyzed using the Pearson χ² test. Receiveroperating characteristic (ROC) curves were generated and the area underthe ROC curve (AUC) was used as a measure of test performance. TheMann-Whitney U test and Kruskall-Wallis test was used to determinedifferences in methylation ratio in 2 groups or more, respectively. Thestudent T test was used to compare positive methylation and age. Tocompare sensitivity and specificity of the patient group referred withabnormal cytology by DNA methylation markers versus hrHPV, the extendedMcNemar test, described by Hawass was executed³². P-values lower than0.05 were considered statistically significant.

Results

Identification of differential methylated genes by MethylCap sequencingGenome-wide MethylCap-seq was used to compare the DNA methylationprofiles of CIN2/3 dysplastic cervical cells with normal cervical cellsto identify CIN2/3 specific DMRs. After applying our criteria, 176 DMRscomprising 163 genes remained (data not shown).

Verification and Validation of the Top15 Differentially Methylated Genes

To verify the MethylCap-seq data, the top 15, out of the 163 identifiedgenes were selected. MSP primers were designed and could be optimizedfor 14 out of the 15 genes. Verification of the selected 14 genes showedfor 11 genes a significant correlation between the MSP band intensityand the amount of reads from the MethylCap-seq data. One gene (PCDH17)showed high methylation levels in leukocytes and was therefore excludedfor further validation. The remaining 10 genes passed verification andcontinued to the subsequent validation step. Table 2 shows an overviewof which genes continued through the different stages of validation.

TABLE 2 Verification, validation and diagnostic evaluation of thehighest ranking top 15 genes. 1^(st) diagnostic 2^(nd) diagnostic RankGene Optimized Verification Validation evaluation evaluation  1 ZSCAN1Yes Yes Yes Yes Yes  2 PCDH17 Yes No*  3 ST6GALNAC5 Yes Yes Yes Yes Yes 4 CLIC6 Yes No  5 AC01234.1 Yes No  6 ANKRD18CP Yes Yes Yes Yes Yes  7PAX2** Yes Yes Yes No  8 CDH6 Yes Yes Yes Yes Yes  9 GFRA1 Yes Yes YesYes Yes 10 IRX1 Yes No 11 POU4F3 Yes Yes No* 12 GATA4 Yes Yes Yes YesYes 13 MKX No 14 PAX2** Yes No 15 KCNIP4 Yes Yes Yes Yes Yes 16 LHX8 YesYes Yes Yes Yes *Excluded due to high methylation in leukocytes **Samegene, different region

The second validation step was performed by MSP on DNA from FFPE tissueof an independent, randomly selected new patient cohort that consistedof 13 cervical cancers, 19 HSIL lesions (8 CIN2, 8 CIN3 and 3 adCIS) and17 normal cervices. Out of the 10 genes analyzed, 9 showed lowmethylation levels in the normal samples, significant differentialmethylation between normal versus HSIL lesions and again little to nomethylation in the leukocytes (p<0.05) (Table 3). These 9 genes (ZSCAN1,ST6GALNAC5, ANKRD18CP, PAX2, CDH6, GFRA1, GATA4, KCNIP4 and LHX8) wereselected for further diagnostic evaluation in cervical scrapings (Table3).

TABLE 3 Methylation positivity in an external cohort of FFPE samples tovalidate results of high methylation in CIN2+ lesions and no methylationin normal cervices of the newly found methylation markers. Gene NormalCIN2 CIN3 adCIS carcinoma ZSCAN1 4/16 8/8 7/8 3/3 12/13 ST6GALNAC5 0/161/6 4/8 2/3  9/12 ANKRD18CP 0/16 1/8 1/7 2/3  6/12 PAX2 1/14 6/8 7/8 3/3 5/13 CDH6 1/15 3/8 4/8 3/3  7/13 GFRA1 0/12 2/8 3/8 2/3 10/12 POU4F3*2/14 6/7 3/7 3/3 11/12 GATA4 0/17 3/8 2/7 3/3 10/13 KCNIP4 0/17 6/8 5/83/3 10/12 LHX8 1/16 3/8 4/8 3/3  7/13 *Excluded due to high methylationin leukocytes

Diagnostic Evaluation by QMSP for Normal Versus Cancer Scrapings

To evaluate the diagnostic value of the new methylation markers,cervical scrapings from two cohorts of patients were used: 1) normalversus carcinoma scrapings and 2) scrapings from patients referred frompopulation-based screening with an abnormal Pap smear (≥Pap2). In cohort1, scrapings of 100 randomly selected cervical carcinoma patients and 89patients with histologically confirmed normal cervices were used. QMSPanalysis showed that the relative levels of DNA methylation were higherin the carcinoma scrapings compared to the normal scrapings for 8 out ofthe 9 selected genes (p<0.001) (FIG. 2). The area under the curve (AUC)for methylation ratio in cervical carcinoma showed for 8 genes anAUC>0.91, and for one gene (PAX2) an AUC of 0.59. Therefore PAX2 wasexcluded from further analysis (FIG. 3). In women with a normal cervix,methylation positivity for all 9 genes was not related to age (data notshown).

Diagnostic Evaluation by QMSP for Normal/LSIL Versus HSIL Scrapings

In cohort 2, scrapings of 215 consecutive patients referred frompopulation-based screening with an abnormal Pap smear were used. The 8genes that showed differential methylation in the normal versus thecancer scrapings were subsequently tested in cohort 2. Methylationlevels and frequencies for all 8 genes analyzed (ZSCAN1, ST6GALNAC5,ANKRD18CP, CDH6, GFRA1, GATA4, KCNIP4 and LHX8), increased with theseverity of the underlying histological lesion (p<0.001) (FIG. 4 andTable 4).

Without setting a cut-off value for achieving higher/lower sensitivityand/or specificity, genes ZSCAN1, ST6GALNAC5 and KCNIP4 reached highsensitivity (>90%) for detection of CIN2+ lesions, while for CDH6, GATA4and LHX8 sensitivity for CIN2+ was between 73-84% (Table 5a). ForANKRD18CP and GFRA1 sensitivity for CIN2+ was between 46-61%, and thesegenes showed especially high specificity (82%-92%). In our analysis, wealso included a marker panel of 4 genes, previously described by ourgroup (C13ORF18, JAM3, EPB41L3 and TERT) to compare sensitivity andspecificity of these known genes with the newly identified methylationmarkers. The gene C13ORF18 showed reproducible results as describedpreviously²¹ with high specificity (95%) and relatively low sensitivityfor CIN2+ of 40%. JAM3 and EPB41L3 showed sensitivities for CIN2+between 63-69% and specificities between 79-91%. The gene TERT waspreviously described with high specificity, but this result could not bereproduced since specificity was only 46% in our analysis, whilesensitivity for CIN2+ lesions was 82%.

hrHPV Status and Triage Testing

HrHPV testing was performed on the patients group referred with abnormalcytology at population-based screening. For 6 out of 215 patientsinsufficient material was available to perform HPV testing. HrHPV wasdetected in 152/209 (73%) samples by the GP5+/6+ PCR and COBAS HPV test.Table 4 shows HPV status in relation to underlying histologicaldiagnosis. HrHPV was present in 12/26 (46%) patients without CIN lesion,24/36 (67%) CIN1 patients, 36/45 (80%) CIN2 patients, 49/59 (83%) CIN3patients and 31/43 (72%) patients with miCa. The sensitivity of hrHPVtesting for CIN2+ was 79% with a specificity of 42%.

TABLE 4 Cytology according to the Papanicolaou system (Bethesda system)per histological subgroup. Methylation and HPV positivity of the 8 newmethylation markers and 4 known markers tested with QMSP in cervicalscrapings from patients with CIN0, CIN1, CIN2, CIN3 and (mi)Ca (n =215). Cytology CIN0 CIN1 CIN2 CIN3 miCA Pap2 (ASCUS)  9/27 (33%)  9/38(24%) 2/45 (4%) 0 0 Pap3A (LSIL) 18/27 (66%) 27/38 (71%) 36/45 (80%)18/61 (30%)  5/44 (11%) Pap3B (HSIL) 0 2/38 (5%)  6/45 (13%) 33/61 (54%)27/44 (61%) Pap4 (HSIL) 0 0 1/45 (2%) 10/61 (16%)  8/44 (18%) Pap5(MiCa) 0 0 0 0 3/44 (7%) Unknown 0 0 0 0 1/44 (2%) New genes ZSCAN120/27 (74%) 28/38 (74%) 41/45 (91%) 55/61 (90%)  44/44 (100%) ST6GALNAC522/27 (82%) 33/38 (87%) 39/45 (84%) 56/61 (92%) 41/44 (93%) ANKRD18CP 3/26 (12%)  8/36 (22%) 20/45 (44%) 33/59 (56%) 37/43 (86%) CDH6 10/26(39%) 15/36 (42%) 25/45 (56%) 40/59 (68%) 42/43 (98%) GFRA1 1/26 (4%) 4/36 (11%)  9/45 (20%) 23/59 (39%) 35/43 (81%) GATA4 14/26 (54%) 21/36(58%) 35/45 (78%) 47/59 (80%) 41/43 (95%) KCNIP4 24/27 (89%) 36/38 (95%)44/45 (98%)  61/61 (100%) 43/44 (98%) LHX8 12/26 (46%) 20/36 (56%) 29/45(64%) 48/59 (81%) 41/43 (95%) Known genes C13ORF18 2/27 (7%) 1/38 (3%) 9/45 (20%) 24/61 (39%) 27/44 (61%) JAM3  3/27 (11%) 3/38 (8%) 18/45(40%) 39/61 (64%) 37/44 (84%) EPB41L3 2/27 (7%) 12/38 (32%) 18/45 (40%)44/61 (72%) 41/44 (93%) TERT 13/27 (48%) 22/38 (58%) 29/45 (64%) 51/61(84%) 43/44 (98%) HPV test HrHPV 12/26 (46%) 24/36 (67%) 36/45 (80%)49/59 (83%) 31/43 (72%)

For the genes CDH6, GATA4, and LHX8 sensitivity and specificity resultswere comparable to hrHPV testing with sensitivity for CIN2+ between73-84% and specificity between 40-60% (Table 5A).

TABLE 5A Sensitivity and specificity results for CIN2+ and CIN3+ incervical scrapings from patients referred from population-basedscreening with an abnormal pap smear (n = 215) Sensitivity SpecificitySensitivity Specificity Gene CIN2+ CIN2+ CIN3+ CIN3+ ZSCAN1 93% 26% 94%19% ST6GALNAC5 90% 15% 92% 16% ANKRD18CP 61% 82% 69% 71% CDH6 73% 60%80% 53% GFRA1 46% 92% 57% 87% GATA4 84% 44% 87% 35% KCNIP4 99%  8% 99% 6% LHX8 80% 40% 87% 43% C13ORF18 40% 95% 49% 89% EPB41L3 69% 79% 81%71% JAM3 63% 91% 72% 78% TERT 82% 46% 90% 42% hrHPV 79% 42% 78% 33%

Table 5B shows sensitivity and specificity for CIN2+ and CIN3+ inscrapings of hrHPV positive women (n=152), which were comparable to theresults for the whole group, as shown in Table 5a. The genes ZSCAN1,ST6GALNAC5 and KCNIP4 again showed high sensitivity (>92%) for thedetection of CIN2+, while for CDH6, GATA4, EPB41L3, TERT and ZSCAN16sensitivity for CIN2+ was between 72-85%. For ANKRD18CP, JAM3, C13ORF18and GFRA1 sensitivity for CIN2+ was between 43-68%, however these genesshowed high specificity between 86-94%. In the current Dutch populationbased screening program, women with pap2/pap3a (ASCUS/LSIL) scrapingsare retested after 6 months with triage testing by hrHPV. Therefore, wealso show the results of triage testing by hrHPV and methylation markersin this group (Table 5B). Triage testing by hrHPV shows a sensitivityfor CIN2+ of 82% with a specificity of 41%; GATA4, LHX8 and TERT showcomparable results.

TABLE 5B Sensitivity and specificity results for CIN2+ and CIN3+ inscrapings of hrHPV positive women (n = 152) and in scraping ofPap2/Pap3a (ASCUS/LSIL) patients (n = 124). Only hrHPV positive patients(n = 152) Sensitivity Specificity Sensitivity Specificity CIN2+ CIN2+CIN3+ CIN3+ ZSCAN1 94% 36% 96% 23% ST6GALNAC5 92% 19% 94% 15% ANKRD18CP65% 86% 74% 71% CDH6 72% 64% 83% 57% GFRA1 51% 92% 64% 85% GATA4 85% 47%88% 33% KCNIP4 98% 11% 99%  7% LHX8 81% 53% 91% 47% C13ORF18 43% 94% 54%88% EPB41L3 72% 78% 85% 68% JAM3 68% 94% 80% 76% TERT 81% 47% 90% 43%Only Pap2/3A patients (n = 124) ZSCAN1 90% 27% 87% 20% ST6GALNAC5 90%16% 96% 15% ANKRD18CP 38% 82% 41% 75% CDH6 58% 59% 73% 56% GFRA1 22% 92%32% 90% GATA4 78% 44% 77% 35% KCNIP4 98%  8% 100%   6% LHX8 70% 49% 86%46% C13ORF18 23% 95% 30% 90% EPB41L3 51% 78% 74% 72% JAM3 44% 91% 57%80% TERT 74% 48% 87% 43% hrHPV 82% 41% 82% 32%

Different combinations of genes were analyzed to find the bestmethylation marker panel with the highest combined sensitivity andspecificity. For this analysis a sample was considered positive ifeither of the genes in the combination tested was positive. By addingmore than 3 genes in a combination specificity of the methylation testdecreased, with minimal increase in sensitivity. The combinations ofgenes with the highest combined sensitivity and specificity for CIN2+was JAM3/ANKRD18CP, C13ORF18/JAM3/ANKRD18CP and JAM3/GFRA1/ANKRD18CPwith a sensitivity of 72%, 74% and 73%, which is comparable to hrHPVtesting (79%). Specificity of both combinations was 71% and 76%, whichis significantly higher than for hrHPV testing (42%) (p≤0.05). Table 6shows that for all other combinations sensitivities for detecting CIN2+lesions are between 64-80%, with a combined specificity between 58-88%.

TABLE 6 Combinations of different methylation markers to create a panelof genes most suited as test in scrapings ranked on highest sensitivity(n = 215). Sensitivity Specificity Sensitivity Specificity Genecombination CIN2+ CIN2+ CIN3+ CIN3+ JAM3/CDH6 80% 58% 85% 48%ANKRD18CP/CDH6/EPB41L3 80% 55% 87% 48% CDH6/EPB41L3 78% 57% 85% 50%GFRA1/EPB41L3/CDH6 78% 57% 85% 50% ANKRD18CP/CDH6 77% 57% 83% 49%GFRA1/ANKRD18CP/CDH6 77% 57% 83% 49% JAM3/EPB41L3/ANKRD18CP 76% 71% 84%60% C13ORF18/JAM3/ANKRD18CP 74% 76% 80% 62% ANKRD18CP/EPB41L3 74% 74%83% 64% GFRA1/EPB41L3/ANKRD18CP 74% 74% 84% 64% C13ORF18/CDH6 74% 58%80% 51% JAM3/GFRA1/ANKRD18CP 73% 77% 80% 64% C13ORF18/JAM3/EPB41L3 73%72% 83% 64% GFRA1/CDH6 73% 60% 80% 53% JAM3/ANKRD18CP 72% 79% 79% 65%JAM3/EPB41L3 72% 75% 83% 66% JAM3/EPB41L3/GFRA1 72% 76% 83% 66%GFRA1/EPB41L3 69% 79% 82% 71% C13ORF18/EPB41L3 69% 75% 81% 68%C13ORF18/JAM3/GFRA1 66% 82% 77% 72% JAM3/GFRA1 65% 86% 76% 75%C13ORF18/ANKRD18CP 65% 79% 72% 67% C13ORF18/JAM3 64% 88% 73% 76%GFRA1/ANKRD18CP 64% 81% 72% 69%

In the hrHPV positive scrapings, the sensitivities and specificities forCN2+ of the 3 best-performing combinations (JAM3/ANKRD8CP,C13ORF18/JAM3/ANKRD18CP and JAM3/GFRA1/ANKRD18CP) were comparable(sensitivity: 76-77%; specificity: 81-83%) (Table 7) to the totalpopulation.

TABLE 7 Combinations of different methylation markers to create a panelof genes most suited as triage test in HPV positive scrapings ranked onhighest sensitivity (n = 152). Sensitivity Specificity SensitivitySpecificity Gene combination CIN2+ CIN2+ CIN3+ CIN3+ JAM3/CDH6 80% 64%88% 50% ANKRD18CP/CDH6/EPB41L3 79% 61% 89% 51% CDH6/EPB41L3 77% 61% 88%53% GFRA1/EPB41L3/CDH6 78% 61% 88% 53% ANKRD18CP/CDH6 77% 61% 85% 51%GFRA1/ANKRD18CP/CDH6 77% 61% 85% 51% JAM3/EPB41L3/ANKRD18CP 78% 72% 88%58% C13ORF18/JAM3/ANKRD18CP 77% 81% 85% 61% ANKRD18CP/EPB41L3 75% 75%86% 63% GFRA1/EPB41L3/ANKRD18CP 75% 75% 86% 63% C13ORF18/CDH6 73% 61%83% 54% JAM3/GFRA1/ANKRD18CP 76% 81% 85% 63% C13ORF18/JAM3/EPB41L3 76%72% 86% 60% GFRA1/CDH6 72% 64% 83% 57% JAM3/ANKRD18CP 76% 83% 85% 64%JAM3/EPB41L3 75% 75% 86% 63% JAM3/EPB41L3/GFRA1 75% 75% 86% 63%GFRA1/EPB41L3 72% 78% 85% 68% C13ORF18/EPB41L3 72% 75% 85% 65%C13ORF18/JAM3/GFRA1 70% 86% 81% 71% JAM3/GFRA1 69% 89% 81% 74%C13ORF18/ANKRD18CP 68% 83% 76% 67% C13ORF18/JAM3 69% 92% 80% 74%GFRA1/ANKRD18CP 67% 83% 76% 68%

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1. A kit for use in identifying a cervical cell as neoplastic orpredisposed to neoplasia in an isolated sample, the kit comprising:methylation specific PCR primers complementary to marker gene C13ORF18,methylation specific PCR primers complementary to marker gene ANKRD18CP,a gene specific probe for marker gene C13ORF18, and a gene specificprobe for marker gene ANKRD18CP.
 2. The kit of claim 1, furthercomprising an Ayre's spatula and/or an endocervical brush for removingcervical cells from a subject.
 3. The kit of claim 1, wherein themethylation specific PCR primers complementary to marker gene ANKRD18CPcomprise a first primer comprising sequence CGATGTGGTATTTTCGATTC (SEQ IDNO: 5) and a second primer comprising sequence ACGTGTAAAAAATCGCCAC (SEQID NO: 6).
 4. The kit of claim 1, wherein the gene specific probe formarker gene ANKRD18CP comprises sequence AGGAGCGTTTGGTTTAGGCGTTTTTCG(SEQ ID NO: 19).
 5. The kit of claim 1, further comprising methylationspecific PCR primers complementary to marker gene ZSCAN1 and a genespecific probe for marker gene ZSCAN1.
 6. The kit of claim 5, whereinthe methylation specific PCR primers complementary to marker gene ZSCAN1comprise a first primer comprising sequence TTGTTGGTATTCGTTTGTTC (SEQ IDNO: 1) and a second primer comprising sequence ACGCGACCGAACGATATT (SEQID NO: 2).
 7. The kit of claim 5, wherein the gene specific probe formarker gene ZSCAN1 comprises sequenceAGGTCGAAGTTTTTTTACGTATTTTTATTGTTCGTTTA (SEQ ID NO: 17).
 8. The kit ofclaim 1, further comprising methylation specific PCR primerscomplementary to marker gene EPB41L3 and a gene specific probe formarker gene EPB41L3.
 9. The kit of claim 1, further comprisingmethylation specific PCR primers complementary to marker gene JAM3 and agene specific probe for marker gene JAM3.
 10. The kit of claim 1,further comprising methylation specific PCR primers complementary tomarker gene KCNIP4 and a gene specific probe for marker gene KCNIP4. 11.The kit of claim 1, further comprising methylation specific PCR primerscomplementary to marker gene GFRA1 and a gene specific probe for markergene GFRA1.
 12. The kit of claim 1, further comprising methylationspecific PCR primers complementary to marker gene ST6GALNAC5 and a genespecific probe for marker gene ST6GALNAC5.
 13. The kit of claim 1,further comprising methylation specific PCR primers complementary tomarker gene CDH6 and a gene specific probe for marker gene CDH6.
 14. Thekit of claim 1, further comprising methylation specific PCR primerscomplementary to marker gene LHX8 and a gene specific probe for markergene LHX8.